You need to call the Javascript function explicitely, after the call.
For that if you are initiating Ajax call from JS function, the you need to call your function after recieving the response from server.
Or
If you are using Updatepanel, the you can register your function as startupscript block as
ScriptManager.RegisterStartupScript(this.Page, typeof(System.Web.UI.Page), "StartupScript", "<script type='text/javascript' language='javascript'>javascript:yourfunction()</script>", false);